The folded modules of aggrecan G3 domain exert two separable functions in glycosaminoglycan modification and product secretion

Aggrecan is the major proteoglycan in the extracellular matrix of cartilage. A notable exception is nanomelic cartilage, which lacks aggrecan in its matrix. The example of nanomelia and other evidence leads us to believe that the G3 domain plays an important role in aggrecan processing, and it has indeed been confirmed that G3 allows glycosaminoglycan (GAG) chain attachment and product secretion. However, it is not clear how G3, which contains at least a carbohydrate recognition domain (CRD) and a complement binding protein (CBP) motif, plays these two functional roles. The present study was designed to dissect the mechanisms of this phenomenon and specially 1) to determine the effects of various cysteine residues in GAG modification and product secretion as well as 2) to investigate which of the two processing events is the critical step in the product processing. Our studies demonstrated that removal of the two amino-terminal cysteines in the CRD motif and the single cysteine in the amino terminus of CBP inhibited secretion of CRD and CBP. Use of the double mutant CRD construct also allowed us to observe a deviation from the usual strict coupling of GAG modification and product secretion steps. The presence of a small chondroitin sulfate fragment overcame the secretion-inhibitory effects once the small chondroitin sulfate fragment was modified by GAG.

Multisite pooling study using ligase chain reaction in screening for genital Chlamydia trachomatis infections

BACKGROUND

Ligase chain reaction (LCR), a nucleic acid amplification assay, is a highly specific and sensitive test for detecting Chlamydia trachomatis in cervical and urethral swabs as well as first-void urine specimens.

GOAL

To examine the suitability of using the LCR test to detect C trachomatis in pooled cervical specimens.

STUDY DESIGN

The performance of LCR in pooled specimens was compared with individual specimen testing at six laboratories using 3,170 cervical swab specimens randomly selected from specimens received for routine testing in the participating laboratories. These samples then were combined consecutively into 634 pools of 5 specimens and 317 pools of 10 specimens. A reduced sample to cutoff ratio of 0.2 or more was used for the pooled specimens.

RESULTS

Of the 188 positive specimens (98.9%), 186 were identified when single specimens were analyzed. When pools of 5 or 10 specimens were evaluated, 99.5% and 98.9% of the positive swabs, respectively, were identified correctly. Two positive specimens were detected only through pooling.

CONCLUSIONS

Pooling samples for detection of C trachomatis by LCR is sensitive and specific. Depending on the prevalence of infection (positivity), LCR testing may result in cost savings, as compared with individual testing of specimens.

An optimized recipe for cloning of the polymerase chain reaction-amplified DNA inserts into plasmid vectors

This study compares a number of parameters that are important in the ligation of the polymerase chain reaction-amplified DNA inserts into plasmid vectors and their efficient transformation to bacterial cells. The parameters covered were: T4 polynucleotide kinase treatment followed by either the large fragment of E. coli DNA polymerase or T4 DNA polymerase reactions, the amount of T4 DNA ligase, temperature and duration of ligation, molar ratio of insert to vector as well as the total DNA concentration. The results show that the T4 polynucleotide kinase-treated group without further enzymatic manipulation, at an insert to vector ratio of 3:1 gave the highest recombination efficiency when 10 microg/ml DNA and 20 units T4 DNA ligase were applied for ligation for 12 h at 4 degrees C.

Integration of PCR fragments at any specific site within cloning vectors without the use of restriction enzymes and DNA ligase

Here, we describe a method that offers a unique way to engineer plasmids with precision but without digestion using restriction enzymes for the insertion of DNA. The method allows the insertion of PCR fragments in between any two nucleotides within a target plasmid. The only requirement is that the amplified fragments must be embedded between DNA sequences homologous to the site in which the integration is planned. This method is an adaptation of the QuikChange Site-Directed Mutagenesis protocol. It is simpler than the existing cloning strategies and is suitable for multiparallel constructions of new plasmids. We have demonstrated its utility by constructing plasmids in which we have successfully integrated PCR fragments up to 1117 bp.

Development of ligase-assisted spacer addition for the measurement of microsatellites

Conventional methods for detecting differences in microsatellite repeat lengths rely on electrophoretic fractionation on long denaturing polyacrylamide gels, a time-consuming and labor-intensive method. Therefore, there is a need for the development of new and rapid approaches to routinely detect such length polymorphisms. The advent of techniques allowing the coupling of DNA molecules to solid surfaces has provided new prospects in the area of mutation detection. We describe here the development and optimization of the ligase-assisted spacer addition (LASA) method, a novel and rapid procedure based on an ELISA format to measure microsatellite repeat lengths. The LASA assay was successfully applied to a set of 11 bird samples to assess its capabilities as a genotyping method.

Impaired repair activity of a truncated DNA polymerase beta protein

DNA polymerase beta (polbeta) is an essential enzyme for gap filling synthesis in damaged DNA template involved in base excision repair pathway. A truncated polbeta protein is expressed in primary colorectal and breast adenocarcinomas. To determine a possible alteration in the functions of the enzyme, a human cell line named HeLapolbetadelta expressing the truncated form of polbeta has been established. These cells revealed a significantly reduced level of repair activity evaluated by gap filling synthesis and polbeta activity. More importantly, the HeLapolbetadelta cells are hypersensitive to MNNG, a DNA alkylating agent. It appears from the responses that the gap filling synthesis of WT cells, a HeLa cell line overexpressing wild-type polbeta protein, was inhibited by HeLapolbetadelta protein.

Synthesis and characterization of a tetranucleotide analogue containing alternating phosphonate-amide backbone linkages

Described herein is the synthesis and characterization of a tetranucleotide, 5'-dC-phosphonate-T-amide-T-ophosphonate-dC (III), in which the C-T and T-C steps contain a phosphonate backbone bond and T-T is a peptide nucleic acid dimer unit (neutral backbone). The 5'- and 3'-OH groups of the tetramer can be further derivatized and, thus, the compound is a potential building block for longer oligonucleotides which will contain alternating backbone modifications at designated positions. The synthesis involved first the preparation of two hybrid peptide-deoxyribose dinucleotides, CT-CO (I) and N-CT (II) (C and T are nucleobases; CO and N are carboxylic and amino terminal, respectively); each is linked through a phosphonate linkage. A condensation reaction between the two dimers, followed by deprotection, resulted in the formation of a peptide linkage to give the desired tetramer III. The reaction conditions used are mild to afford products in moderate to excellent yields. The DNA-PNA-DNA tetramer, d(CTTC), is a substrate for T4 kinase but fails to give a ligation product, even though NMR shows weak interactions between the tetramer III with its complementary sequence, d(GAAG).

Microarray hybridization with fractionated cDNA: enhanced identification of differentially expressed genes

Molecular indexing is a technique to select a subpopulation of cDNA by ligation of adapters to cDNA fragments digested by a class IIS restriction enzyme(s). By this technique, 3' end cDNA fragments are divided into 16 fractions by selective ligation of adapters and subsequent PCR amplification. Each fraction is used as a hybridization target for microarray hybridization. This fractionated target has a relatively lower nucleic acid complexity, including more fractions for rare transcripts, and is useful for their detection. In an experiment with mouse cerebellum and cerebrum RNA, analysis of a subset of candidate genes indicated that 10 times more differentially expressed genes were detected by this method than by the conventional method using the unfractionated target.

The Preterm Prediction Study: association of second-trimester genitourinary chlamydia infection with subsequent spontaneous preterm birth

OBJECTIVE

This study was undertaken to determine the association between genitourinary tract infection with Chlamydia trachomatis and spontaneous preterm birth.

STUDY DESIGN

Genitourinary tract infection with C trachomatis was determined with a ligase chain reaction assay of voided urine samples collected at 24 weeks' gestation (22 weeks' to 24 weeks 6 days' gestation) and 28 weeks' gestation (27 weeks' to 28 weeks 6 days' gestation). Case patients (spontaneous preterm birth at <37 weeks' gestation; n = 190) and control subjects (delivery at >/=37 weeks' gestation, matched for race, parity, and center; n = 190) were selected from 2929 women enrolled in the Preterm Prediction Study of the National Institute of Child Health and Human Development Maternal-Fetal Medicine Units Network.

RESULTS

Genitourinary C trachomatis infection (11% overall) was significantly more common among the case patients than among the control subjects at 24 weeks' gestation (15.8% vs 6.3%; P =.003) but not at 28 weeks' gestation (12.6% vs 10.9%; P =.61). Women with chlamydia infection were more likely to have bacterial vaginosis (57.1% vs 32.9%; P =.002) and a short cervical length (</=25 mm; 33.0% vs 17.9%; P =.02) but not a body mass index <19.8 kg/m(2) (35.0% vs 23.9%; P =.17) or a positive fetal fibronectin test result (7.1% vs 9.5%; P =.62). After adjustment for risk factors for spontaneous preterm birth, women with C trachomatis infection at 24 weeks' gestation were 2 times as likely as uninfected women to have a spontaneous preterm birth at <37 weeks' gestation (odds ratio, 2.2; 95% confidence interval, 1.03-4.78) and 3 times as likely to have a spontaneous preterm birth at <35 weeks' gestation (odds ratio, 3.2; 95% confidence interval, 1.08-9.57).

CONCLUSION

Genitourinary C trachomatis infection at 24 weeks' gestation was associated with a 2-fold to 3-fold increased risk of subsequent spontaneous preterm birth.

Pooling cervical swabs and testing by ligase chain reaction are accurate and cost-saving strategies for diagnosis of Chlamydia trachomatis

Specimen pooling to achieve efficiency when testing urine specimens for Chlamydia trachomatis nucleic acids has been suggested. We pooled endocervical swabs from 1,288 women and also tested individual swabs by ligase chain reaction (LCR). Out of 53 positive specimens, pools of 4 or 8 specimens missed two positives, providing 96.2% accuracy compared to individual test results. Dilution and positive-control spiking experiments showed that negative specimens with inhibitors of LCR in the pool reduced the signal. Conversely, two extra positives, detected only through pooling, were negative by individual testing but became positive after storage, suggesting that fresh positive specimens with labile inhibitors may be positive in a pool because of dilution of inhibitors. For this population of women with a 4% prevalence of C. trachomatis infection, substantial savings in cost of reagents (55 to 63%) and technologist time (50 to 63%) made pooling strategies a desirable alternative to individual testing.

Improved method for detecting differentially expressed genes using cDNA indexing

In cDNA indexing, differentially expressed genes are identified by the display of specific, corresponding subsets of cDNA. Subdivision of the cDNA population is achieved by the sequence-specific ligation of adapters to the overhangs created by class IIS restriction enzymes. However, inadequate specificity of ligation leads to redundancy between different adapter subsets. We evaluate the incidence of mismatches between adapters and class IIS restriction fragments during ligation and describe a modified set of conditions that improves ligation specificity. The improved protocol reduces redundancy between amplified cDNA subsets, which leads to a lower number of bands per lane of the differential display gel, and therefore simplifies analysis. We confirm the validity of this revised protocol by identifying five differentially expressed genes in mouse duodenum and ileum.

Mutation detection in K-ras, BRCA1, BRCA2, and p53 using PCR/LDR and a universal DNA microarray

We have developed a multiplex PCR/ligase detection reaction (PCR/LDR) that combines high sensitivity with the ability to simultaneously detect hundreds of mutations in a single-tube reaction. To enable us to rapidly assay large numbers of samples, we have linked this mutation detection scheme with analysis on a Universal DNA microarray. We have successfully applied this approach to characterize K-ras and p53 mutations in DNA derived from undissected colon tumors. The sensitivity of the assay has also facilitated detection of low-frequency mutations in BRCA1 and BRCA2 in pooled samples of DNA; thus, PCR/LDR can rapidly screen large numbers of DNA samples required for population studies.

Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications

DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor. Despite the difference in cofactor specificity and limited overall sequence similarity, the two classes of DNA ligase share basically the same catalytic mechanism. In this study, the crystal structure of an NAD(+)-dependent DNA ligase from Thermus filiformis, a 667 residue multidomain protein, has been determined by the multiwavelength anomalous diffraction (MAD) method. It reveals highly modular architecture and a unique circular arrangement of its four distinct domains. It also provides clues for protein flexibility and DNA-binding sites. A model for the multidomain ligase action involving large conformational changes is proposed.

Evaluation of self-taken samples for the presence of genital Chlamydia trachomatis infection in women using the ligase chain reaction assay

The aim of this study was to evaluate the sensitivity and acceptability of self-taken vulval-introital (VI) samples, first-catch urine (FCU) samples and clinician-obtained cervical samples for the presence of genital Chlamydia trachomatis infections in women using the ligase chain reaction (LCR) assay. One hundred and four patients were enrolled, of whom 54 patients had chlamydial DNA in at least one of the samples tested. The sensitivity of the cervical sample was 96.3%, vulval-introital sample in LCR buffer 92.6%, vulval-introital swab collected dry 88.9%, FCU stored at +2-8 degrees C 81.5%, FCU stored at room temperature 77.8% and FCU stored with 2% w/v boric acid at room temperature 87.0%. Self-taken vulval-introital LCR samples were shown to be an acceptable alternative to a clinician-obtained LCR sample. The addition of boric acid may overcome the need for a continuous cold chain for FCU samples.

Specific inhibition of the eubacterial DNA ligase by arylamino compounds

All known DNA ligases catalyze the formation of a phosphodiester linkage between adjacent termini in double-stranded DNA via very similar mechanisms. The ligase family can, however, be divided into two classes: eubacterial ligases, which require NAD(+) as a cofactor, and other ligases, from viruses, archaea, and eukaryotes, which use ATP. Drugs that discriminate between DNA ligases from different sources may have antieubacterial activity. We now report that a group of arylamino compounds, including some commonly used antimalarial and anti-inflammatory drugs and a novel series of bisquinoline compounds, are specific inhibitors of eubacterial DNA ligases. Members of this group of inhibitors have different heterocyclic ring systems with a common amino side chain in which the two nitrogens are separated by four carbon atoms. The potency, but not the specificity of action, is influenced by the DNA-binding characteristics of the inhibitor, and the inhibition is noncompetitive with respect to NAD(+). The arylamino compounds appear to target eubacterial DNA ligase in vivo, since a Salmonella Lig(-) strain that has been rescued with the ATP-dependent T4 DNA ligase is less sensitive than the parental Salmonella strain.

Control of Chlamydia trachomatis infections in female army recruits: cost-effective screening and treatment in training cohorts to prevent pelvic inflammatory disease

CONTEXT

Chlamydia trachomatis genitourinary infections in females can lead to serious and costly sequelae. Programs such as basic (initial entry) military training with controlled points of entry offer an opportunity to screen large cohorts of women at risk for infection.

OBJECTIVE

To assess the cost-effectiveness of three interventions for C. trachomatis infections in women beginning Army training: 1) screening using urine ligase chain reaction (LCR) by age, 2) unrestricted testing using urine LCR, and 3) universal antibiotic treatment with azithromycin.

DESIGN

Cost-effectiveness analysis from a military perspective.

SETTING AND PATIENTS

A hypothetical cohort of 10,000 women who intended to complete at least 2 years of military service was studied. Analysis was based on data from 13,204 female trainees screened for chlamydial infection at Fort Jackson, SC.

OUTCOMES

Program and training costs, cost of illness averted, and pelvic inflammatory disease (PID) prevented were determined for a 1-year follow-up period. Using sensitivity analysis, outcomes over 2 years were studied.

RESULTS

At a 9.2% prevalence, no screening resulted in $220,900 in training and sequelae costs and 276 cases of PID. Screening by age produced the lowest cost $217,600, over a 1-year period and prevented 222 cases of PID for a cost-savings of $15 per case of PID prevented. Universal testing prevented an additional 11 cases of PID at a cost of $226,400, or costing $800 per additional case of PID prevented over age-targeted screening. Universal treatment prevented an additional 32 cases of PID and cost $221,100, saving $167 per additional cases of PID prevented over universal screening. Over a 2-year period, universal treatment provided the highest cost-savings and prevented the most disease.

CONCLUSION

Screening by age provided a cost-savings to the Army over a 1-year period. Other organizations accessing large cohorts of young women could also benefit, even in the short term, from implementation of an age-based chlamydial screening program. Universal testing or universal treatment may be warranted in which long-term societal goals, such as maximum reduction of PID, are relevant.

The impact on accuracy and cost of ligase chain reaction testing by pooling urine specimens for the diagnosis of Chlamydia trachomatis infections

BACKGROUND AND OBJECTIVES

Nucleic acid amplification testing is the most accurate approach to diagnosing Chlamydia trachomatis infections. Our objective was to compare the accuracy and cost savings of pooling urines as opposed to individual testing.

STUDY DESIGN

Strategies of pooling urine specimens into groups of four (4x pool) or eight (8x pool) followed by testing the positive pools individually were compared to individual specimen testing to determine if significant cost savingS could be realized without compromising the sensitivity and specificity of the LCx C. trachomatis Assay (Abbott Laboratories, Abbott Park, Chicago, IL) performed in a busy private medical laboratory.

RESULTS

A total of 1,220 patient urine samples, 1,187 male (97%) and 33 female (3%), were tested using the normal LCx specimen to cutoff ratio (S/CO) of 1.0 and a decreased S/CO value of 0.2. Individual testing identified 98.2% (109/111) of positive urines. The 4x pooling maneuver identified 92.8% (103/111) of positive patients with the regular cutoff and 96.4% (107/111) when the cutoff was decreased. These values were 95.9% (47/49) and 97.9% (48/49), respectively, when eight urines were pooled. Both pooling and individual testing strategies identified all the negative samples accurately. Cost savings of pooling were calculated to be 44.5% for pools of four and 37.5% for pools of eight, applying the lowered cutoff.

CONCLUSIONS

Pooling urine specimens for testing with the C. trachomatis LCx system is a simple, accurate, and cost-saving approach that can significantly reduce the cost of amplified nucleic acid testing with minimal sacrifice of testing accuracy.

Multicenter evaluation of the Abbott LCx Mycobacterium tuberculosis ligase chain reaction assay

Four Australian hospital laboratories evaluated the performance of the Abbott LCx Mycobacterium tuberculosis assay with 2,347 specimens (2,083 respiratory and 264 nonrespiratory specimens) obtained from 1, 411 patients. A total of 152 specimens (6.5%) were culture positive for Mycobacterium tuberculosis complex (MTBC); of these, 79 (52%) were smear positive. After resolution of discrepant data, the overall sensitivity, specificity, and positive and negative predictive values for the LCx assay were 69.7, 99.9, 99.1, and 97.7% respectively. For smear-positive respiratory specimens that were culture positive for MTBC, the values were 98.5, 100, 100, and 98.4%, respectively, while the values for smear-negative respiratory specimens were 41.5, 99.9, 96.4, and 98%, respectively. Relative operating characteristic curves were constructed to demonstrate the relationship between sensitivity and specificity for a range of possible cutoff values in the LCx assay. These graphs suggested that the assay sensitivity for respiratory samples could be increased from 70.2 to 78.6%, while the specificity would be reduced from 99.9 to 99.4% by inclusion of a grey zone (i.e., LCx assay values of between 0.2 and 0.99). An algorithm is presented for the handling of specimens with LCx assay values within this grey zone.

Detection of Mycobacterium bovis in bovine tissue samples by the Abbott LCx Mycobacterium tuberculosis assay and comparison with culture methods

A ligase chain reaction (LCR) DNA amplification method for the molecular diagnosis of Mycobacterium tuberculosis complex (Abbott LCx MTB) was evaluated in comparison with solid (Lowenstein Jensen), liquid (7H12, Bactec 460 system) phase culture and microscopic examination (ME) on 86 tissue samples collected from 86 intradermal tuberculin positive cattle and one pool from 4 guinea pigs experimentally infected with M. bovis. Overall, 48 samples (58.81%) were culturally positive for mycobacteria, and on the basis of biochemical characters, all the isolates were identified as M. bovis. Sensitivity was 83.92% for LCx, 53.57% for LJ, 85.71% for Bactec and 41.07% for ME. In 3 out of 25 "no visible lesion" tissue samples, M. bovis was detected only by LCx and Bactec but not by LJ and ME. The concordance in the determination of positives and negatives among the methods observed in pairs was calculated according to Cohen's K concordance coefficient and showed 81.1% of concordance of LCx vs Bactec, 68.8% LCx vs LJ, 72.2% LCx vs ME, 80.0% Bactec vs LJ, 66.7% Bactec vs ME, 85.5% LJ vs ME. Despite a certain variability in concordance rates, both Cohen's K concordance coefficients or standardized (Zk) values were statistically significant. Both LCx and Bactec appear not alternative but subsidiary to the other methods traditionally applied for direct diagnosis of bovine tuberculosis on tissue samples from cattle reacting to intradermal tuberculin test.

Impact of menstrual cycle on the diagnostic performance of LCR, TMA, and PCE for detection of Chlamydia trachomatis in home obtained and mailed vaginal flush and urine samples

OBJECTIVES

To assess the impact of the menstrual cycle on the diagnostic performance of various assays for detection of Chlamydia trachomatis in home obtained and mailed vaginal flush and urine specimens.

METHODS

A ligase chain reaction assay (LCR; Abbott Laboratories), a transcription mediated amplification assay (TMA; Gen-Probe), and an enzyme amplified immunoassay (PCE; Dako Diagnostics) were evaluated for their validity in detecting C trachomatis in vaginal flush, first void urine, and midstream urine specimens obtained by female high school students at home and mailed directly to the diagnostic laboratory.

RESULTS

C trachomatis was detected in 45 of 889 females (5.1%). The vaginal flush material was positive by TMA and LCR in 84% and 82% of the chlamydia positive females, respectively. First void urine was positive by TMA in 73% and by LCR in 49% of the cases. Midstream urine was positive by TMA and LCR in 69% and 42% of the females, respectively. On a pool of first void and midstream urine, PCE detected 49% of the chlamydia positive females. The overall prevalence of C trachomatis increased with increasing time after the last menstrual bleeding. In urine samples, but not vaginal flush specimens, obtained 3 weeks after the last menstrual bleeding, the sensitivities of TMA, LCR, and PCE decreased markedly suggesting that inhibitors to the assays are excreted in the urine but not in vaginal secretions at this time.

CONCLUSION

Vaginal flush samples are superior to urines for detection of chlamydia infections in females. In screening of young asymptomatic females, samples should be obtained in the latter part of the menstrual cycle.

Comparison of the sensitivity and specificity of an automatic ligase chain reaction assay system with a one-step polymerase chain reaction assay in the diagnosis of Mycobacterium tuberculosis complex

BACKGROUND

Polymerase chain reaction (PCR) and ligase chain reaction (LCR) are two nucleic acid amplification-based molecular methods. The former has been used widely in the identification of Mycobacterium tuberculosis (M. tuberculosis). In contrast, the LCR assay which was recently introduced is not well known in our medical communities in Taiwan. To determine which method is more reliable and suitable for the identification of M. tuberculosis in our clinics, we compared the sensitivity and specificity of these two methods.

METHODS

An automatic LCR assay system and a manual one-step PCR assay were studied in a side by side comparison of their performance in detection of M. tuberculosis. The automatic LCR system uses the single copy antigen protein b (Pab) gene and the manual one-step PCR assay uses the multi-copy IS6110 insertion element as the target DNA; both target DNA sequences are found specifically in M. tuberculosis complex.

RESULTS

Both assays detected two of the M. tuberculosis complex strains, M. tuberculosis and M. bovis, but not other mycobacterial strains. In addition, both methods, which were based on different amplification principles, showed compatible sensitivity; as low as 10 and 100 copies of M. tuberculosis genomes were detected by the LCR and PCR assays, respectively. When the template DNA was less than 1000 copies, however, the automatic LCR assay system showed a lower reproducibility than that of the one-step PCR assay.

CONCLUSION

Our results suggest that in addition to the PCR assay, the LCR assay is a useful method for the molecular identification of M. tuberculosis complex strains.

Amplification of closed circular DNA in vitro

The polymerase chain reaction is a powerful technique used to amplify nucleic acids in vitro. The reaction produces linear products, and as of yet, closed circular products have not been possible. Since the replicatively competent form of many DNA molecules is the closed circular form, it would be adventitious to amplify closed circular DNA as closed circular molecules. Until now, these molecules could only be amplified in vivo in appropriate host cells. Here, we describe an in vito procedure, ligation-during-amplification (LDA), for selective amplification of closed circular DNA using sequence-specific primers. LDA is useful for site-directed mutagenesis, mutation detection, DNA modification, DNA library screening and circular DNA production.